Contacts of the strand formed by residues 428 - 431 (chain C) in PDB entry 1T5A
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 428 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C ALA* 4.3 10.3 - - + +
417C VAL* 4.4 3.1 - - - -
420C SER* 3.9 32.3 - - - +
427C ALA* 1.3 80.4 - - - +
429C ILE* 1.3 62.9 + - - +
430C VAL* 3.6 21.8 + - + +
441C VAL* 3.8 29.2 - - + -
446C PRO* 4.0 17.5 - - + -
448C ALA* 4.7 5.6 - - + -
449C PRO 3.0 9.2 + - - +
450C ILE* 3.4 7.0 - - + -
451C ILE 3.1 19.5 + - - -
510C ILE* 3.3 20.0 - - + +
512C LEU* 4.7 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 429 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C ALA* 5.0 0.4 - - + -
428C ILE* 1.3 73.0 - - - +
430C VAL* 1.3 59.3 + - - +
431C LEU* 4.5 11.0 - - + -
451C ILE* 3.5 18.2 - - + +
453C VAL* 4.6 1.1 - - + -
490C VAL* 4.2 9.2 - - + +
493C ALA* 3.6 35.7 - - + -
494C MET* 3.8 31.4 - - + +
503C PHE* 4.6 5.4 - - + -
509C VAL* 3.7 22.9 - - + -
510C ILE 2.7 12.6 + - - +
511C VAL* 4.2 17.5 - - + -
512C LEU* 2.7 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 430 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C ILE* 3.7 24.9 - - + +
429C ILE* 1.3 81.2 - - - +
431C LEU* 1.3 76.3 + - - +
432C THR* 3.6 1.3 + - - -
437C SER* 3.9 23.3 - - - -
438C ALA* 4.1 17.7 - - + +
441C VAL* 4.3 4.5 - - + -
450C ILE* 3.9 13.2 - - + -
451C ILE 2.9 11.7 + - - +
452C ALA* 3.4 4.1 - - - +
453C VAL 2.7 28.2 + - - -
512C LEU* 3.8 24.9 - - + -
522C THR* 5.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 431 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C ILE* 4.5 7.9 - - + -
430C VAL* 1.3 83.9 - - - +
432C THR* 1.3 64.2 + - - +
437C SER* 4.2 2.1 - - - -
453C VAL* 3.6 10.1 - - + +
486C VAL* 3.8 28.7 - - + -
489C ARG* 3.7 42.8 - - + +
490C VAL* 3.6 32.8 - - + +
512C LEU 3.3 15.5 + - - +
513C THR* 4.4 3.1 - - + -
522C THR* 4.4 2.1 + - - +
532C FBP 3.2 37.6 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il